Open BioSource HTGAA 20 - Week 1 assignment Goals & Rationale - - PowerPoint PPT Presentation

Open BioSource

HTGAA 20’ - Week 1 assignment

Goals & Rationale

• Inspired by Software Engineering - Open Source philosophy and ecosystem
• “given enough eyeballs, all bugs are shallow" (Linus’s law)
• Software bugs are analogous to risky bio workflows.
• Open vs. closed source security is a matter of active debate.
• Creators share readable code (-> workflow), the community can flag issues, and suggest practical

fixes (“merges/pull requests”)

• Open Source Mentality - BioHackers should document their workflow and be open to sharing as

well as accepting suggestions for improvements.

• Open Source Ecosystem - BioHackers should have access to a suite of tools that will allow

comfortable recording of workflows, including detailed history of changes to the workflow, and be able to share and receive feedback.

• The goal is to prevent hazardous workflows, for the biohacker or the environment.

Design & Requirements

• 1. Mentality:

○ Education - in events such as iGEM ○ Create a common language for protocols and workflows ○ Reward active community members

• 2. Ecosystem:

○ Electronic Lab Notebooks (ELNs) - right now there are a plethora of solutions (e.g. Benchling) yet a lot of researchers still use paper notebooks (Kwok 2018) ○ Adapting a common protocol to be used by all ELNs ○ BioGithub - easy access to a repository full of community-vetted workflows ○ Documenting your workflow should be easy and not add any extra labour to an already labour-full project ○ Smart Lab - a lab can be equipped with simple sensors that will log each machine use, thus automatically creating an almost workflow for an experiment

Principles:

• Reproducible
• Auditable
• Contributable

Assumptions & Risks

• Sharing private workflows might lead to:
• Research Plagiarism (scooping)
• Misuse of sensitive, dangerous biotechnology
• Only works if there’s a strong active community
• Mentality cannot be implemented without the proper tools and ecosystem, and vice versa -

chicken and egg.